Antibiootikumiresistentsus omavahel seotud tehislikus ja looduslikus veekeskkonnas

Väitekirja elektrooniline versioon ei sisalda publikatsiooneAntibiootikumid on kõige olulisemad bakteriaalsete infektsioonide ravimiseks mõeldud ained, kuid kõikide antibiootikumide vastu tekib bakteritel ühel hetkel resistentsus, st et antibiootikum ei suuda enam bakterit tappa. Nii on antibiootikumiresistentsusest kujunenud tänapäeval üks suurimaid tervishoiuprobleeme maailmas. See ei ole siiski ainult meditsiinisektori probleem, vaid selle tekke ja leviku taga on ka antibiootikumide kasutamine põllumajanduses ja loomakasvatuses. Reoveepuhastusjaamade heitvesi on üks peamisi teid, kuidas resistentsus tehiskeskkonnast looduslikku keskkonda pääseb, kuna reoveepuhastuse käigus ei eemaldata kõiki antibiootikumijääke, resistentseid baktereid ega ka antibiootikumiresistentsust põhjustavaid geene. Kuna reoveepuhastusjaamade heitvesi juhitakse enamasti looduslikesse veekogudesse, näiteks ojadesse või jõgedesse, suureneb resistentsusnäitajate arv reoveepuhasti väljavoolust allavoolu jäävatel aladel. Antibiootikumiresistentsed bakterid ja resistentsusgeenid võivad kanduda edasi põhjavette, jõgedesse ja lõpuks ka merre. Sealt võivad need omakorda inimesele tagasi kanduda, näiteks saastunud vett juues, mereande süües või ujudes. Siinse doktoritöö eesmärgiks oli kirjeldada, kuidas reoveepuhastusjaamast pärinevad antibiootikumiresistentsusgeenid levivad allavoolu jäävasse ojja, sealt edasi jõkke ning viimaks Läänemerre. Töö tulemustest selgus, et reoveepuhastusjaamal on kõige suurem mõju vahetus läheduses (0,3 kilomeetrit) oleva veekeskkonna mikroobikoosluse struktuurile ja antibiootikumiresistentsusgeenide arvukusele. Samas juba 3,7 kilomeetrit eemal oli jõe bakterikooslus võrreldav reoveepuhastist ülesvoolu jääva alaga. Siiski tulenevalt Läänemere eripäradest – suur reostuskoormus, tihe rannikuala asustatus, suur valgala, aeglane veevahetus, madal vesi – on merekeskkond väga tundlik antibiootikumiresistentsusgeenide reostuse suhtes.Antibiotic resistance in connected engineered and natural aquatic environments Antibiotics are the most important drugs for treating bacterial infections, but all antibiotics introduced are susceptible to resistance, which means that the antibiotic no longer kills the bacteria. Thus, antibiotic resistance has become one of the biggest human health problems in the world today. Antibiotic resistance is not only a problem in medicine, but the use of antibiotics in agriculture and animal husbandry also play an important role in the spread of antibiotic resistance. Wastewater treatment plants effluent is one of the main pathways by which the resistance determinants from the human environment are introduced to the natural environment, because not all antibiotic residues, resistant bacteria and antibiotic resistance encoding genes are removed during wastewater treatment process. Since wastewater treatment plants effluent is often discharged into natural waterbodies, such as streams and rivers, the number of resistance determinants in downstream water increases. Antibiotic resistant bacteria and resistance genes can be transmitted to groundwater, rivers and ultimately to the sea, from where they can also be transmitted back to humans - for example, by drinking contaminated water, eating seafood or swimming. The aim of this thesis was to describe the dissemination pathway of the antibiotic resistance genes originating from the wastewater treatment plant effluent through the primary receiving waterbody to the final receiving waterbody (Baltic Sea). The results indicated that the wastewater treatment plant has the greatest impact on the aquatic environment in the close vicinity (0.3 kilometers) of the effluent as already 3.7 kilometers downstream the bacterial community of the river was comparable to the area upstream of the wastewater treatment plant effluent. However, the Baltic Sea is very vulnerable to ARG contamination due to its specifics (long water retention time, shallowness, large catchment area, high pollution load).https://www.ester.ee/record=b546564

Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure,dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater.The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently,the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation.The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.publishedVersio

Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure,dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater.The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently,the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation.The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe